On Fri, Apr 11, 2014 at 1:13 PM, newamber list <newamberlist.gmail.com> wrote:
> Finally one thing, as now I am using a nonimaged traj with 'reference' , so
> 'radial' will consider the imaged or nonimaged referenced frame?
The radial command will image distances whenever periodic boundary
conditions (i.e. box information) are present in the trajectory unless
'noimage' is specified. The 'reference' keyword in no way affects
'radial'.
-Dan
>
> reference test.nc 10
> trajin test.nc 10 10
> radial rdf.dat 0.1 10 :WAT (:484,441,382,213>.100&.Cl-) volume
>
> thanks
> JIomm
>
>
> On Fri, Apr 11, 2014 at 7:33 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
>> Hi,
>>
>> I can't reproduce the behavior you are seeing. When I generate similar
>> plots, I get a nice overlap between single RDFs and averaged RDF (see
>> attached). I don't think this would be an averaging bug anyway - the
>> fact that you get population at the lower distance bins means the
>> underlying histogram had some data there. If you are absolutely
>> certain none of those distances should be shorter than 2 Ang., the
>> only thing I can think of is maybe you are using a trajectory with
>> periodic boundary conditions that has been rotated e.g. via an RMS
>> fit, which would cause imaging artifacts. What happens if you specify
>> 'noimage' to the 'radial' command?
>>
>> -Dan
>>
>>
>> On Thu, Apr 10, 2014 at 4:08 PM, newamber list <newamberlist.gmail.com>
>> wrote:
>> > Hi All
>> >
>> > I am getting some unusual rdf starting at zero distances of ion which is
>> > wrong and I think could be an averaging problem. Here is a single frame
>> > command. (and plot attached)
>> >
>> > reference test.nc 10
>> >
>> > trajin test.nc 10 10
>> >
>> > radial rdf.dat 0.1 10 :WAT (:484,441,382,213>.100&.Cl-) volume
>> >
>> >
>> > Actually this should give me an average RDF for all the Cl- ions which
>> are
>> > 100 Ang. distance far from COM of :484,441,382,213. There should be no
>> RDF
>> > values below distance 2 or so. But when I test the same with some
>> > individual Cl- ions (>100 Angs) with masks like this for individual
>> ion:WAT
>> > :3740, I don't get any such RDF near distance zero which is correct.
>> >
>> >
>> > So I think there is some averaging bug?
>> >
>> >
>> > Thanks
>> >
>> > Jiomm
>> >
>> > _______________________________________________
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>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>>
>>
>> --
>> -------------------------
>> Daniel R. Roe, PhD
>> Department of Medicinal Chemistry
>> University of Utah
>> 30 South 2000 East, Room 201
>> Salt Lake City, UT 84112-5820
>> http://home.chpc.utah.edu/~cheatham/
>> (801) 587-9652
>> (801) 585-6208 (Fax)
>>
>> _______________________________________________
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Fri Apr 11 2014 - 13:00:02 PDT
